Invalid cross-device link in razzo_project scripts

[richelbilderbeek]

Same as raket Issue 43

Did:

sbatch scripts/1_install_razzo.sh 
sbatch scripts/2_create_parameter_files.sh test
sbatch scripts/3_run_razzo.sh 

Errors:

Rscript -e razzo::run_razzo_from_file("./data/0.2-0.15-1-0.1/2/parameters.RDa")
Registered S3 method overwritten by 'geiger':
  method            from
  unique.multiPhylo ape 
Error in value[[3L]](cond) : Could not estimate the marginal likelihood. 
Error message: File 'output_log_filename' not found. Could not find file with path '/local/tmp/RtmpcLWmdk/filed98b6f883bd7.log'
site_model$name: JC69
clock_model$name: strict
tree_prior$name: birth_death
epsilon: 1e-12
rng_seed: 2
verbose: FALSE
beast2_working_dir: /home/p230198/.cache/file2c1f9726c83cc/pff_2c1f946886f6b
beast2_bin_path: /home/p230198/.local/share/beast/bin/beast
Calls: <Anonymous> ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
In addition: Warning messages:
1: In file.rename(from = actual_log_filename, to = output_log_filename) :
  cannot rename file '/home/p230198/.cache/file2c1f9726c83cc/pff_2c1f946886f6b/mbd_evidence.log' to '/local/tmp/RtmpcLWmdk/filed98b6f883bd7.log', reason 'Invalid cross-device link'
2: In file.rename(from = actual_trees_filename, to = to) :
  cannot rename file '/home/p230198/.cache/file2c1f9726c83cc/pff_2c1f946886f6b/mbd_evidence.trees' to '/local/tmp/RtmpcLWmdk/filed98b4b82e747.trees', reason 'Invalid cross-device link'
Execution halted


###############################################################################
Peregrine Cluster
Job 7426906 for user 'p230198'
Finished at: Fri Aug 23 15:23:40 CEST 2019

Job details:
============

Name                : run_r_cmd
User                : p230198
Partition           : regular
Nodes               : pg-node031
Cores               : 1
State               : FAILED
Submit              : 2019-08-23T15:22:20
Start               : 2019-08-23T15:23:17
End                 : 2019-08-23T15:23:40
Reserved walltime   : 20:00:00
Used walltime       : 00:00:23
Used CPU time       : 00:00:20 (efficiency: 88.43%)
% User (Computation): 89.22%
% System (I/O)      : 10.78%
Mem reserved        : 10G/node
Max Mem used        : 0.00  (pg-node031)
Max Disk Write      : 0.00  (pg-node031)
Max Disk Read       : 0.00  (pg-node031)


Acknowledgements:
=================

Please see this page if you want to acknowledge Peregrine in your publications:

https://redmine.hpc.rug.nl/redmine/projects/peregrine/wiki/ScientificOutput

[richelbilderbeek]

Will try again:

p230198@peregrine:razzo_project ls
DESCRIPTION  LICENSE  pics  README.md  scripts
p230198@peregrine:razzo_project sbatch scripts/1_install_razzo.sh 
Submitted batch job 7443037
p230198@peregrine:razzo_project sbatch --dependency=afterok:7443037 scripts/2_create_parameter_files.sh test
Submitted batch job 7443038
p230198@peregrine:razzo_project sbatch --dependency=afterok:7443038 scripts/3_run_razzo.sh 
Submitted batch job 7443039

[richelbilderbeek]

Still fails for the same reason:

Rscript -e razzo::run_razzo_from_file("./data/0.2-0.15-1-0.1/2/parameters.RDa")
Registered S3 method overwritten by 'geiger':
  method            from
  unique.multiPhylo ape 
Error in value[[3L]](cond) : Could not estimate the marginal likelihood. 
Error message: File 'output_log_filename' not found. Could not find file with path '/local/tmp/RtmpeGPSW5/file5656296131fe.log'
site_model$name: JC69
clock_model$name: strict
tree_prior$name: birth_death
epsilon: 1e-12
rng_seed: 2
verbose: FALSE
beast2_working_dir: /home/p230198/.cache/file20a2a3cd46428/pff_20a2a5c391b4e
beast2_bin_path: /home/p230198/.local/share/beast/bin/beast
Calls: <Anonymous> ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
In addition: Warning messages:
1: In file.rename(from = actual_log_filename, to = output_log_filename) :
  cannot rename file '/home/p230198/.cache/file20a2a3cd46428/pff_20a2a5c391b4e/mbd_evidence.log' to '/local/tmp/RtmpeGPSW5/file5656296131fe.log', reason 'Invalid cross-device link'
2: In file.rename(from = actual_trees_filename, to = to) :
  cannot rename file '/home/p230198/.cache/file20a2a3cd46428/pff_20a2a5c391b4e/mbd_evidence.trees' to '/local/tmp/RtmpeGPSW5/file565630d0d824.trees', reason 'Invalid cross-device link'
Execution halted


###############################################################################
Peregrine Cluster
Job 7443041 for user 'p230198'
Finished at: Tue Aug 27 11:05:39 CEST 2019

Job details:
============

Name                : run_r_cmd
User                : p230198
Partition           : regular
Nodes               : pg-node027
Cores               : 1
State               : FAILED
Submit              : 2019-08-27T11:05:18
Start               : 2019-08-27T11:05:18
End                 : 2019-08-27T11:05:39
Reserved walltime   : 20:00:00
Used walltime       : 00:00:21
Used CPU time       : 00:00:19 (efficiency: 91.84%)
% User (Computation): 89.61%
% System (I/O)      : 10.39%
Mem reserved        : 10G/node
Max Mem used        : 0.00  (pg-node027)
Max Disk Write      : 0.00  (pg-node027)
Max Disk Read       : 0.00  (pg-node027)

[richelbilderbeek]

p230198@peregrine:razzo_project cp data/0.2-0.15-1-0.1/2/parameters.RDa ~

p230198@peregrine:razzo_project cd ~

p230198@peregrine:~ logout
Connection to peregrine.hpc.rug.nl closed.

richel@sonic:~/GitHubs/raket$ scp p230198@peregrine.hpc.rug.nl:/home/p230198/parameters.RDa .

richel@sonic:~/GitHubs/raket$ zip issue_3.zip parameters.RDa 
  adding: parameters.RDa (stored 0%)

issue_3.zip

[richelbilderbeek]

Nope, this is not the cause of the parameter file itself:

Rscript -e 'params <- readRDS("~/parameters.RDa"); params' | clip

$mbd_params
$mbd_params$lambda
[1] 0.2

$mbd_params$mu
[1] 0.15

$mbd_params$nu
[1] 1

$mbd_params$q
[1] 0.1

$mbd_params$cond
[1] 1

$mbd_params$crown_age
[1] 6

$mbd_params$seed
[1] 2


$pir_params
$pir_params$twinning_params
$pir_params$twinning_params$rng_seed_twin_tree
[1] 0

$pir_params$twinning_params$rng_seed_twin_alignment
[1] 0

$pir_params$twinning_params$twin_model
[1] "birth_death"

$pir_params$twinning_params$method
[1] "random_tree"

$pir_params$twinning_params$n_replicates
[1] 10000

$pir_params$twinning_params$twin_tree_filename
[1] "/home/p230198/GitHubs/razzo_project/data/0.2-0.15-1-0.1/2/mbd_twin.tree"

$pir_params$twinning_params$twin_alignment_filename
[1] "/home/p230198/GitHubs/razzo_project/data/0.2-0.15-1-0.1/2/mbd_twin.fasta"

$pir_params$twinning_params$twin_evidence_filename
[1] "/home/p230198/GitHubs/razzo_project/data/0.2-0.15-1-0.1/2/mbd_marg_lik_twin.csv"


$pir_params$alignment_params
$pir_params$alignment_params$root_sequence
[1] "aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggtttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttttt"

$pir_params$alignment_params$mutation_rate
[1] 0.08333333

$pir_params$alignment_params$site_model
$pir_params$alignment_params$site_model$name
[1] "JC69"

$pir_params$alignment_params$site_model$id
[1] NA

$pir_params$alignment_params$site_model$gamma_site_model
$pir_params$alignment_params$site_model$gamma_site_model$gamma_cat_count
[1] "0"

$pir_params$alignment_params$site_model$gamma_site_model$gamma_shape
[1] "1.0"

$pir_params$alignment_params$site_model$gamma_site_model$prop_invariant
[1] "0.0"

$pir_params$alignment_params$site_model$gamma_site_model$gamma_shape_prior_distr
[1] NA



$pir_params$alignment_params$clock_model
$pir_params$alignment_params$clock_model$name
[1] "strict"

$pir_params$alignment_params$clock_model$id
[1] NA

$pir_params$alignment_params$clock_model$clock_rate_param
$pir_params$alignment_params$clock_model$clock_rate_param$name
[1] "clock_rate"

$pir_params$alignment_params$clock_model$clock_rate_param$id
[1] NA

$pir_params$alignment_params$clock_model$clock_rate_param$value
[1] "1.0"

$pir_params$alignment_params$clock_model$clock_rate_param$estimate
[1] FALSE


$pir_params$alignment_params$clock_model$clock_rate_distr
$pir_params$alignment_params$clock_model$clock_rate_distr$name
[1] "uniform"

$pir_params$alignment_params$clock_model$clock_rate_distr$id
[1] NA

$pir_params$alignment_params$clock_model$clock_rate_distr$upper
[1] Inf



$pir_params$alignment_params$rng_seed
[1] 2

$pir_params$alignment_params$fasta_filename
[1] "/home/p230198/GitHubs/razzo_project/data/0.2-0.15-1-0.1/2/mbd.fasta"


$pir_params$experiments
$pir_params$experiments[[1]]
$pir_params$experiments[[1]]$inference_conditions
$pir_params$experiments[[1]]$inference_conditions$model_type
[1] "generative"

$pir_params$experiments[[1]]$inference_conditions$run_if
[1] "always"

$pir_params$experiments[[1]]$inference_conditions$do_measure_evidence
[1] TRUE


$pir_params$experiments[[1]]$inference_model
$pir_params$experiments[[1]]$inference_model$site_model
$pir_params$experiments[[1]]$inference_model$site_model$name
[1] "JC69"

$pir_params$experiments[[1]]$inference_model$site_model$id
[1] NA

$pir_params$experiments[[1]]$inference_model$site_model$gamma_site_model
$pir_params$experiments[[1]]$inference_model$site_model$gamma_site_model$gamma_cat_count
[1] "0"

$pir_params$experiments[[1]]$inference_model$site_model$gamma_site_model$gamma_shape
[1] "1.0"

$pir_params$experiments[[1]]$inference_model$site_model$gamma_site_model$prop_invariant
[1] "0.0"

$pir_params$experiments[[1]]$inference_model$site_model$gamma_site_model$gamma_shape_prior_distr
[1] NA



$pir_params$experiments[[1]]$inference_model$clock_model
$pir_params$experiments[[1]]$inference_model$clock_model$name
[1] "strict"

$pir_params$experiments[[1]]$inference_model$clock_model$id
[1] NA

$pir_params$experiments[[1]]$inference_model$clock_model$clock_rate_param
$pir_params$experiments[[1]]$inference_model$clock_model$clock_rate_param$name
[1] "clock_rate"

$pir_params$experiments[[1]]$inference_model$clock_model$clock_rate_param$id
[1] NA

$pir_params$experiments[[1]]$inference_model$clock_model$clock_rate_param$value
[1] "1.0"

$pir_params$experiments[[1]]$inference_model$clock_model$clock_rate_param$estimate
[1] FALSE


$pir_params$experiments[[1]]$inference_model$clock_model$clock_rate_distr
$pir_params$experiments[[1]]$inference_model$clock_model$clock_rate_distr$name
[1] "uniform"

$pir_params$experiments[[1]]$inference_model$clock_model$clock_rate_distr$id
[1] NA

$pir_params$experiments[[1]]$inference_model$clock_model$clock_rate_distr$upper
[1] Inf



$pir_params$experiments[[1]]$inference_model$tree_prior
$pir_params$experiments[[1]]$inference_model$tree_prior$name
[1] "birth_death"

$pir_params$experiments[[1]]$inference_model$tree_prior$id
[1] NA

$pir_params$experiments[[1]]$inference_model$tree_prior$birth_rate_distr
$pir_params$experiments[[1]]$inference_model$tree_prior$birth_rate_distr$name
[1] "uniform"

$pir_params$experiments[[1]]$inference_model$tree_prior$birth_rate_distr$id
[1] NA

$pir_params$experiments[[1]]$inference_model$tree_prior$birth_rate_distr$upper
[1] Inf


$pir_params$experiments[[1]]$inference_model$tree_prior$death_rate_distr
$pir_params$experiments[[1]]$inference_model$tree_prior$death_rate_distr$name
[1] "uniform"

$pir_params$experiments[[1]]$inference_model$tree_prior$death_rate_distr$id
[1] NA

$pir_params$experiments[[1]]$inference_model$tree_prior$death_rate_distr$upper
[1] Inf



$pir_params$experiments[[1]]$inference_model$mrca_prior
$pir_params$experiments[[1]]$inference_model$mrca_prior$name
[1] NA

$pir_params$experiments[[1]]$inference_model$mrca_prior$alignment_id
[1] NA

$pir_params$experiments[[1]]$inference_model$mrca_prior$taxa_names
[1] NA

$pir_params$experiments[[1]]$inference_model$mrca_prior$is_monophyletic
[1] TRUE

$pir_params$experiments[[1]]$inference_model$mrca_prior$mrca_distr
$pir_params$experiments[[1]]$inference_model$mrca_prior$mrca_distr$name
[1] "normal"

$pir_params$experiments[[1]]$inference_model$mrca_prior$mrca_distr$id
[1] NA

$pir_params$experiments[[1]]$inference_model$mrca_prior$mrca_distr$mean
$pir_params$experiments[[1]]$inference_model$mrca_prior$mrca_distr$mean$name
[1] "mean"

$pir_params$experiments[[1]]$inference_model$mrca_prior$mrca_distr$mean$id
[1] NA

$pir_params$experiments[[1]]$inference_model$mrca_prior$mrca_distr$mean$value
[1] 6

$pir_params$experiments[[1]]$inference_model$mrca_prior$mrca_distr$mean$estimate
[1] FALSE


$pir_params$experiments[[1]]$inference_model$mrca_prior$mrca_distr$sigma
$pir_params$experiments[[1]]$inference_model$mrca_prior$mrca_distr$sigma$name
[1] "sigma"

$pir_params$experiments[[1]]$inference_model$mrca_prior$mrca_distr$sigma$id
[1] NA

$pir_params$experiments[[1]]$inference_model$mrca_prior$mrca_distr$sigma$value
[1] 1e-04

$pir_params$experiments[[1]]$inference_model$mrca_prior$mrca_distr$sigma$estimate
[1] FALSE



$pir_params$experiments[[1]]$inference_model$mrca_prior$clock_prior_distr_id
[1] NA


$pir_params$experiments[[1]]$inference_model$mcmc
$pir_params$experiments[[1]]$inference_model$mcmc$chain_length
[1] 3000

$pir_params$experiments[[1]]$inference_model$mcmc$store_every
[1] 1000


$pir_params$experiments[[1]]$inference_model$beauti_options
$pir_params$experiments[[1]]$inference_model$beauti_options$capitalize_first_char_id
[1] FALSE

$pir_params$experiments[[1]]$inference_model$beauti_options$nucleotides_uppercase
[1] FALSE

$pir_params$experiments[[1]]$inference_model$beauti_options$beast2_version
[1] "2.4"

$pir_params$experiments[[1]]$inference_model$beauti_options$required
[1] ""

$pir_params$experiments[[1]]$inference_model$beauti_options$sequence_indent
[1] 20


$pir_params$experiments[[1]]$inference_model$tipdates_filename
[1] NA


$pir_params$experiments[[1]]$beast2_options
$pir_params$experiments[[1]]$beast2_options$input_filename
[1] "/home/p230198/GitHubs/razzo_project/data/0.2-0.15-1-0.1/2/mbd_gen.xml"

$pir_params$experiments[[1]]$beast2_options$output_log_filename
[1] "/home/p230198/GitHubs/razzo_project/data/0.2-0.15-1-0.1/2/mbd_gen.log"

$pir_params$experiments[[1]]$beast2_options$output_trees_filenames
[1] "/home/p230198/GitHubs/razzo_project/data/0.2-0.15-1-0.1/2/mbd_gen.trees"

$pir_params$experiments[[1]]$beast2_options$output_state_filename
[1] "/home/p230198/GitHubs/razzo_project/data/0.2-0.15-1-0.1/2/mbd_gen.xml.state"

$pir_params$experiments[[1]]$beast2_options$rng_seed
[1] 2

$pir_params$experiments[[1]]$beast2_options$n_threads
[1] NA

$pir_params$experiments[[1]]$beast2_options$use_beagle
[1] FALSE

$pir_params$experiments[[1]]$beast2_options$overwrite
[1] TRUE

$pir_params$experiments[[1]]$beast2_options$beast2_working_dir
[1] "/home/p230198/.cache/file20a2a3cd46428/pff_20a2a5c391b4e"

$pir_params$experiments[[1]]$beast2_options$beast2_path
[1] "/home/p230198/.local/share/beast/lib/launcher.jar"

$pir_params$experiments[[1]]$beast2_options$verbose
[1] FALSE


$pir_params$experiments[[1]]$est_evidence_mcmc
$pir_params$experiments[[1]]$est_evidence_mcmc$chain_length
[1] 1e+06

$pir_params$experiments[[1]]$est_evidence_mcmc$store_every
[1] 1000

$pir_params$experiments[[1]]$est_evidence_mcmc$particle_count
[1] 1

$pir_params$experiments[[1]]$est_evidence_mcmc$sub_chain_length
[1] 5000

$pir_params$experiments[[1]]$est_evidence_mcmc$epsilon
[1] 1e-12


$pir_params$experiments[[1]]$beast2_bin_path
[1] "/home/p230198/.local/share/beast/bin/beast"

$pir_params$experiments[[1]]$errors_filename
[1] "/home/p230198/GitHubs/razzo_project/data/0.2-0.15-1-0.1/2/mbd_nltts_gen.csv"


$pir_params$experiments[[2]]
$pir_params$experiments[[2]]$inference_conditions
$pir_params$experiments[[2]]$inference_conditions$model_type
[1] "candidate"

$pir_params$experiments[[2]]$inference_conditions$run_if
[1] "best_candidate"

$pir_params$experiments[[2]]$inference_conditions$do_measure_evidence
[1] TRUE


$pir_params$experiments[[2]]$inference_model
$pir_params$experiments[[2]]$inference_model$site_model
$pir_params$experiments[[2]]$inference_model$site_model$name
[1] "HKY"

$pir_params$experiments[[2]]$inference_model$site_model$id
[1] NA

$pir_params$experiments[[2]]$inference_model$site_model$gamma_site_model
$pir_params$experiments[[2]]$inference_model$site_model$gamma_site_model$gamma_cat_count
[1] "0"

$pir_params$experiments[[2]]$inference_model$site_model$gamma_site_model$gamma_shape
[1] "1.0"

$pir_params$experiments[[2]]$inference_model$site_model$gamma_site_model$prop_invariant
[1] "0.0"

$pir_params$experiments[[2]]$inference_model$site_model$gamma_site_model$gamma_shape_prior_distr
[1] NA


$pir_params$experiments[[2]]$inference_model$site_model$kappa
[1] "2.0"

$pir_params$experiments[[2]]$inference_model$site_model$kappa_prior_distr
$pir_params$experiments[[2]]$inference_model$site_model$kappa_prior_distr$name
[1] "log_normal"

$pir_params$experiments[[2]]$inference_model$site_model$kappa_prior_distr$id
[1] NA

$pir_params$experiments[[2]]$inference_model$site_model$kappa_prior_distr$m
$pir_params$experiments[[2]]$inference_model$site_model$kappa_prior_distr$m$name
[1] "m"

$pir_params$experiments[[2]]$inference_model$site_model$kappa_prior_distr$m$id
[1] NA

$pir_params$experiments[[2]]$inference_model$site_model$kappa_prior_distr$m$value
[1] "1.0"

$pir_params$experiments[[2]]$inference_model$site_model$kappa_prior_distr$m$estimate
[1] FALSE


$pir_params$experiments[[2]]$inference_model$site_model$kappa_prior_distr$s
$pir_params$experiments[[2]]$inference_model$site_model$kappa_prior_distr$s$name
[1] "s"

$pir_params$experiments[[2]]$inference_model$site_model$kappa_prior_distr$s$id
[1] NA

$pir_params$experiments[[2]]$inference_model$site_model$kappa_prior_distr$s$value
[1] 1.25

$pir_params$experiments[[2]]$inference_model$site_model$kappa_prior_distr$s$estimate
[1] FALSE

$pir_params$experiments[[2]]$inference_model$site_model$kappa_prior_distr$s$lower
[1] 0

$pir_params$experiments[[2]]$inference_model$site_model$kappa_prior_distr$s$upper
[1] Inf



$pir_params$experiments[[2]]$inference_model$site_model$freq_equilibrium
[1] "estimated"


$pir_params$experiments[[2]]$inference_model$clock_model
$pir_params$experiments[[2]]$inference_model$clock_model$name
[1] "strict"

$pir_params$experiments[[2]]$inference_model$clock_model$id
[1] NA

$pir_params$experiments[[2]]$inference_model$clock_model$clock_rate_param
$pir_params$experiments[[2]]$inference_model$clock_model$clock_rate_param$name
[1] "clock_rate"

$pir_params$experiments[[2]]$inference_model$clock_model$clock_rate_param$id
[1] NA

$pir_params$experiments[[2]]$inference_model$clock_model$clock_rate_param$value
[1] "1.0"

$pir_params$experiments[[2]]$inference_model$clock_model$clock_rate_param$estimate
[1] FALSE


$pir_params$experiments[[2]]$inference_model$clock_model$clock_rate_distr
$pir_params$experiments[[2]]$inference_model$clock_model$clock_rate_distr$name
[1] "uniform"

$pir_params$experiments[[2]]$inference_model$clock_model$clock_rate_distr$id
[1] NA

$pir_params$experiments[[2]]$inference_model$clock_model$clock_rate_distr$upper
[1] Inf



$pir_params$experiments[[2]]$inference_model$tree_prior
$pir_params$experiments[[2]]$inference_model$tree_prior$name
[1] "yule"

$pir_params$experiments[[2]]$inference_model$tree_prior$id
[1] NA

$pir_params$experiments[[2]]$inference_model$tree_prior$birth_rate_distr
$pir_params$experiments[[2]]$inference_model$tree_prior$birth_rate_distr$name
[1] "uniform"

$pir_params$experiments[[2]]$inference_model$tree_prior$birth_rate_distr$id
[1] NA

$pir_params$experiments[[2]]$inference_model$tree_prior$birth_rate_distr$upper
[1] Inf



$pir_params$experiments[[2]]$inference_model$mrca_prior
$pir_params$experiments[[2]]$inference_model$mrca_prior$name
[1] NA

$pir_params$experiments[[2]]$inference_model$mrca_prior$alignment_id
[1] NA

$pir_params$experiments[[2]]$inference_model$mrca_prior$taxa_names
[1] NA

$pir_params$experiments[[2]]$inference_model$mrca_prior$is_monophyletic
[1] TRUE

$pir_params$experiments[[2]]$inference_model$mrca_prior$mrca_distr
$pir_params$experiments[[2]]$inference_model$mrca_prior$mrca_distr$name
[1] "normal"

$pir_params$experiments[[2]]$inference_model$mrca_prior$mrca_distr$id
[1] NA

$pir_params$experiments[[2]]$inference_model$mrca_prior$mrca_distr$mean
$pir_params$experiments[[2]]$inference_model$mrca_prior$mrca_distr$mean$name
[1] "mean"

$pir_params$experiments[[2]]$inference_model$mrca_prior$mrca_distr$mean$id
[1] NA

$pir_params$experiments[[2]]$inference_model$mrca_prior$mrca_distr$mean$value
[1] 6

$pir_params$experiments[[2]]$inference_model$mrca_prior$mrca_distr$mean$estimate
[1] FALSE


$pir_params$experiments[[2]]$inference_model$mrca_prior$mrca_distr$sigma
$pir_params$experiments[[2]]$inference_model$mrca_prior$mrca_distr$sigma$name
[1] "sigma"

$pir_params$experiments[[2]]$inference_model$mrca_prior$mrca_distr$sigma$id
[1] NA

$pir_params$experiments[[2]]$inference_model$mrca_prior$mrca_distr$sigma$value
[1] 1e-04

$pir_params$experiments[[2]]$inference_model$mrca_prior$mrca_distr$sigma$estimate
[1] FALSE



$pir_params$experiments[[2]]$inference_model$mrca_prior$clock_prior_distr_id
[1] NA


$pir_params$experiments[[2]]$inference_model$mcmc
$pir_params$experiments[[2]]$inference_model$mcmc$chain_length
[1] 3000

$pir_params$experiments[[2]]$inference_model$mcmc$store_every
[1] 1000


$pir_params$experiments[[2]]$inference_model$beauti_options
$pir_params$experiments[[2]]$inference_model$beauti_options$capitalize_first_char_id
[1] FALSE

$pir_params$experiments[[2]]$inference_model$beauti_options$nucleotides_uppercase
[1] FALSE

$pir_params$experiments[[2]]$inference_model$beauti_options$beast2_version
[1] "2.4"

$pir_params$experiments[[2]]$inference_model$beauti_options$required
[1] ""

$pir_params$experiments[[2]]$inference_model$beauti_options$sequence_indent
[1] 20


$pir_params$experiments[[2]]$inference_model$tipdates_filename
[1] NA


$pir_params$experiments[[2]]$beast2_options
$pir_params$experiments[[2]]$beast2_options$input_filename
[1] "/home/p230198/GitHubs/razzo_project/data/0.2-0.15-1-0.1/2/mbd_best.xml"

$pir_params$experiments[[2]]$beast2_options$output_log_filename
[1] "/home/p230198/GitHubs/razzo_project/data/0.2-0.15-1-0.1/2/mbd_best.log"

$pir_params$experiments[[2]]$beast2_options$output_trees_filenames
[1] "/home/p230198/GitHubs/razzo_project/data/0.2-0.15-1-0.1/2/mbd_best.trees"

$pir_params$experiments[[2]]$beast2_options$output_state_filename
[1] "/home/p230198/GitHubs/razzo_project/data/0.2-0.15-1-0.1/2/mbd_best.xml.state"

$pir_params$experiments[[2]]$beast2_options$rng_seed
[1] 2

$pir_params$experiments[[2]]$beast2_options$n_threads
[1] NA

$pir_params$experiments[[2]]$beast2_options$use_beagle
[1] FALSE

$pir_params$experiments[[2]]$beast2_options$overwrite
[1] TRUE

$pir_params$experiments[[2]]$beast2_options$beast2_working_dir
[1] "/home/p230198/.cache/file20a2a1fc5d3f8/pff_20a2a3121ac3f"

$pir_params$experiments[[2]]$beast2_options$beast2_path
[1] "/home/p230198/.local/share/beast/lib/launcher.jar"

$pir_params$experiments[[2]]$beast2_options$verbose
[1] FALSE


$pir_params$experiments[[2]]$est_evidence_mcmc
$pir_params$experiments[[2]]$est_evidence_mcmc$chain_length
[1] 1e+06

$pir_params$experiments[[2]]$est_evidence_mcmc$store_every
[1] 1000

$pir_params$experiments[[2]]$est_evidence_mcmc$particle_count
[1] 1

$pir_params$experiments[[2]]$est_evidence_mcmc$sub_chain_length
[1] 5000

$pir_params$experiments[[2]]$est_evidence_mcmc$epsilon
[1] 1e-12


$pir_params$experiments[[2]]$beast2_bin_path
[1] "/home/p230198/.local/share/beast/bin/beast"

$pir_params$experiments[[2]]$errors_filename
[1] "/home/p230198/GitHubs/razzo_project/data/0.2-0.15-1-0.1/2/mbd_nltts_best.csv"


$pir_params$experiments[[3]]
$pir_params$experiments[[3]]$inference_conditions
$pir_params$experiments[[3]]$inference_conditions$model_type
[1] "candidate"

$pir_params$experiments[[3]]$inference_conditions$run_if
[1] "best_candidate"

$pir_params$experiments[[3]]$inference_conditions$do_measure_evidence
[1] TRUE


$pir_params$experiments[[3]]$inference_model
$pir_params$experiments[[3]]$inference_model$site_model
$pir_params$experiments[[3]]$inference_model$site_model$name
[1] "TN93"

$pir_params$experiments[[3]]$inference_model$site_model$id
[1] NA

$pir_params$experiments[[3]]$inference_model$site_model$gamma_site_model
$pir_params$experiments[[3]]$inference_model$site_model$gamma_site_model$gamma_cat_count
[1] "0"

$pir_params$experiments[[3]]$inference_model$site_model$gamma_site_model$gamma_shape
[1] "1.0"

$pir_params$experiments[[3]]$inference_model$site_model$gamma_site_model$prop_invariant
[1] "0.0"

$pir_params$experiments[[3]]$inference_model$site_model$gamma_site_model$gamma_shape_prior_distr
[1] NA


$pir_params$experiments[[3]]$inference_model$site_model$kappa_1_prior_distr
$pir_params$experiments[[3]]$inference_model$site_model$kappa_1_prior_distr$name
[1] "log_normal"

$pir_params$experiments[[3]]$inference_model$site_model$kappa_1_prior_distr$id
[1] NA

$pir_params$experiments[[3]]$inference_model$site_model$kappa_1_prior_distr$m
$pir_params$experiments[[3]]$inference_model$site_model$kappa_1_prior_distr$m$name
[1] "m"

$pir_params$experiments[[3]]$inference_model$site_model$kappa_1_prior_distr$m$id
[1] NA

$pir_params$experiments[[3]]$inference_model$site_model$kappa_1_prior_distr$m$value
[1] 1

$pir_params$experiments[[3]]$inference_model$site_model$kappa_1_prior_distr$m$estimate
[1] FALSE


$pir_params$experiments[[3]]$inference_model$site_model$kappa_1_prior_distr$s
$pir_params$experiments[[3]]$inference_model$site_model$kappa_1_prior_distr$s$name
[1] "s"

$pir_params$experiments[[3]]$inference_model$site_model$kappa_1_prior_distr$s$id
[1] NA

$pir_params$experiments[[3]]$inference_model$site_model$kappa_1_prior_distr$s$value
[1] 1.25

$pir_params$experiments[[3]]$inference_model$site_model$kappa_1_prior_distr$s$estimate
[1] FALSE

$pir_params$experiments[[3]]$inference_model$site_model$kappa_1_prior_distr$s$lower
[1] 0

$pir_params$experiments[[3]]$inference_model$site_model$kappa_1_prior_distr$s$upper
[1] Inf



$pir_params$experiments[[3]]$inference_model$site_model$kappa_2_prior_distr
$pir_params$experiments[[3]]$inference_model$site_model$kappa_2_prior_distr$name
[1] "log_normal"

$pir_params$experiments[[3]]$inference_model$site_model$kappa_2_prior_distr$id
[1] NA

$pir_params$experiments[[3]]$inference_model$site_model$kappa_2_prior_distr$m
$pir_params$experiments[[3]]$inference_model$site_model$kappa_2_prior_distr$m$name
[1] "m"

$pir_params$experiments[[3]]$inference_model$site_model$kappa_2_prior_distr$m$id
[1] NA

$pir_params$experiments[[3]]$inference_model$site_model$kappa_2_prior_distr$m$value
[1] 1

$pir_params$experiments[[3]]$inference_model$site_model$kappa_2_prior_distr$m$estimate
[1] FALSE


$pir_params$experiments[[3]]$inference_model$site_model$kappa_2_prior_distr$s
$pir_params$experiments[[3]]$inference_model$site_model$kappa_2_prior_distr$s$name
[1] "s"

$pir_params$experiments[[3]]$inference_model$site_model$kappa_2_prior_distr$s$id
[1] NA

$pir_params$experiments[[3]]$inference_model$site_model$kappa_2_prior_distr$s$value
[1] 1.25

$pir_params$experiments[[3]]$inference_model$site_model$kappa_2_prior_distr$s$estimate
[1] FALSE

$pir_params$experiments[[3]]$inference_model$site_model$kappa_2_prior_distr$s$lower
[1] 0

$pir_params$experiments[[3]]$inference_model$site_model$kappa_2_prior_distr$s$upper
[1] Inf



$pir_params$experiments[[3]]$inference_model$site_model$kappa_1_param
$pir_params$experiments[[3]]$inference_model$site_model$kappa_1_param$name
[1] "kappa_1"

$pir_params$experiments[[3]]$inference_model$site_model$kappa_1_param$id
[1] NA

$pir_params$experiments[[3]]$inference_model$site_model$kappa_1_param$value
[1] "2.0"

$pir_params$experiments[[3]]$inference_model$site_model$kappa_1_param$lower
[1] "0.0"

$pir_params$experiments[[3]]$inference_model$site_model$kappa_1_param$estimate
[1] TRUE


$pir_params$experiments[[3]]$inference_model$site_model$kappa_2_param
$pir_params$experiments[[3]]$inference_model$site_model$kappa_2_param$name
[1] "kappa_2"

$pir_params$experiments[[3]]$inference_model$site_model$kappa_2_param$id
[1] NA

$pir_params$experiments[[3]]$inference_model$site_model$kappa_2_param$value
[1] "2.0"

$pir_params$experiments[[3]]$inference_model$site_model$kappa_2_param$lower
[1] "0.0"

$pir_params$experiments[[3]]$inference_model$site_model$kappa_2_param$estimate
[1] TRUE


$pir_params$experiments[[3]]$inference_model$site_model$freq_equilibrium
[1] "estimated"


$pir_params$experiments[[3]]$inference_model$clock_model
$pir_params$experiments[[3]]$inference_model$clock_model$name
[1] "strict"

$pir_params$experiments[[3]]$inference_model$clock_model$id
[1] NA

$pir_params$experiments[[3]]$inference_model$clock_model$clock_rate_param
$pir_params$experiments[[3]]$inference_model$clock_model$clock_rate_param$name
[1] "clock_rate"

$pir_params$experiments[[3]]$inference_model$clock_model$clock_rate_param$id
[1] NA

$pir_params$experiments[[3]]$inference_model$clock_model$clock_rate_param$value
[1] "1.0"

$pir_params$experiments[[3]]$inference_model$clock_model$clock_rate_param$estimate
[1] FALSE


$pir_params$experiments[[3]]$inference_model$clock_model$clock_rate_distr
$pir_params$experiments[[3]]$inference_model$clock_model$clock_rate_distr$name
[1] "uniform"

$pir_params$experiments[[3]]$inference_model$clock_model$clock_rate_distr$id
[1] NA

$pir_params$experiments[[3]]$inference_model$clock_model$clock_rate_distr$upper
[1] Inf



$pir_params$experiments[[3]]$inference_model$tree_prior
$pir_params$experiments[[3]]$inference_model$tree_prior$name
[1] "yule"

$pir_params$experiments[[3]]$inference_model$tree_prior$id
[1] NA

$pir_params$experiments[[3]]$inference_model$tree_prior$birth_rate_distr
$pir_params$experiments[[3]]$inference_model$tree_prior$birth_rate_distr$name
[1] "uniform"

$pir_params$experiments[[3]]$inference_model$tree_prior$birth_rate_distr$id
[1] NA

$pir_params$experiments[[3]]$inference_model$tree_prior$birth_rate_distr$upper
[1] Inf



$pir_params$experiments[[3]]$inference_model$mrca_prior
$pir_params$experiments[[3]]$inference_model$mrca_prior$name
[1] NA

$pir_params$experiments[[3]]$inference_model$mrca_prior$alignment_id
[1] NA

$pir_params$experiments[[3]]$inference_model$mrca_prior$taxa_names
[1] NA

$pir_params$experiments[[3]]$inference_model$mrca_prior$is_monophyletic
[1] TRUE

$pir_params$experiments[[3]]$inference_model$mrca_prior$mrca_distr
$pir_params$experiments[[3]]$inference_model$mrca_prior$mrca_distr$name
[1] "normal"

$pir_params$experiments[[3]]$inference_model$mrca_prior$mrca_distr$id
[1] NA

$pir_params$experiments[[3]]$inference_model$mrca_prior$mrca_distr$mean
$pir_params$experiments[[3]]$inference_model$mrca_prior$mrca_distr$mean$name
[1] "mean"

$pir_params$experiments[[3]]$inference_model$mrca_prior$mrca_distr$mean$id
[1] NA

$pir_params$experiments[[3]]$inference_model$mrca_prior$mrca_distr$mean$value
[1] 6

$pir_params$experiments[[3]]$inference_model$mrca_prior$mrca_distr$mean$estimate
[1] FALSE


$pir_params$experiments[[3]]$inference_model$mrca_prior$mrca_distr$sigma
$pir_params$experiments[[3]]$inference_model$mrca_prior$mrca_distr$sigma$name
[1] "sigma"

$pir_params$experiments[[3]]$inference_model$mrca_prior$mrca_distr$sigma$id
[1] NA

$pir_params$experiments[[3]]$inference_model$mrca_prior$mrca_distr$sigma$value
[1] 1e-04

$pir_params$experiments[[3]]$inference_model$mrca_prior$mrca_distr$sigma$estimate
[1] FALSE



$pir_params$experiments[[3]]$inference_model$mrca_prior$clock_prior_distr_id
[1] NA


$pir_params$experiments[[3]]$inference_model$mcmc
$pir_params$experiments[[3]]$inference_model$mcmc$chain_length
[1] 3000

$pir_params$experiments[[3]]$inference_model$mcmc$store_every
[1] 1000


$pir_params$experiments[[3]]$inference_model$beauti_options
$pir_params$experiments[[3]]$inference_model$beauti_options$capitalize_first_char_id
[1] FALSE

$pir_params$experiments[[3]]$inference_model$beauti_options$nucleotides_uppercase
[1] FALSE

$pir_params$experiments[[3]]$inference_model$beauti_options$beast2_version
[1] "2.4"

$pir_params$experiments[[3]]$inference_model$beauti_options$required
[1] ""

$pir_params$experiments[[3]]$inference_model$beauti_options$sequence_indent
[1] 20


$pir_params$experiments[[3]]$inference_model$tipdates_filename
[1] NA


$pir_params$experiments[[3]]$beast2_options
$pir_params$experiments[[3]]$beast2_options$input_filename
[1] "/home/p230198/GitHubs/razzo_project/data/0.2-0.15-1-0.1/2/mbd_best.xml"

$pir_params$experiments[[3]]$beast2_options$output_log_filename
[1] "/home/p230198/GitHubs/razzo_project/data/0.2-0.15-1-0.1/2/mbd_best.log"

$pir_params$experiments[[3]]$beast2_options$output_trees_filenames
[1] "/home/p230198/GitHubs/razzo_project/data/0.2-0.15-1-0.1/2/mbd_best.trees"

$pir_params$experiments[[3]]$beast2_options$output_state_filename
[1] "/home/p230198/GitHubs/razzo_project/data/0.2-0.15-1-0.1/2/mbd_best.xml.state"

$pir_params$experiments[[3]]$beast2_options$rng_seed
[1] 2

$pir_params$experiments[[3]]$beast2_options$n_threads
[1] NA

$pir_params$experiments[[3]]$beast2_options$use_beagle
[1] FALSE

$pir_params$experiments[[3]]$beast2_options$overwrite
[1] TRUE

$pir_params$experiments[[3]]$beast2_options$beast2_working_dir
[1] "/home/p230198/.cache/file20a2a1164bba0/pff_20a2a267c275c"

$pir_params$experiments[[3]]$beast2_options$beast2_path
[1] "/home/p230198/.local/share/beast/lib/launcher.jar"

$pir_params$experiments[[3]]$beast2_options$verbose
[1] FALSE


$pir_params$experiments[[3]]$est_evidence_mcmc
$pir_params$experiments[[3]]$est_evidence_mcmc$chain_length
[1] 1e+06

$pir_params$experiments[[3]]$est_evidence_mcmc$store_every
[1] 1000

$pir_params$experiments[[3]]$est_evidence_mcmc$particle_count
[1] 1

$pir_params$experiments[[3]]$est_evidence_mcmc$sub_chain_length
[1] 5000

$pir_params$experiments[[3]]$est_evidence_mcmc$epsilon
[1] 1e-12


$pir_params$experiments[[3]]$beast2_bin_path
[1] "/home/p230198/.local/share/beast/bin/beast"

$pir_params$experiments[[3]]$errors_filename
[1] "/home/p230198/GitHubs/razzo_project/data/0.2-0.15-1-0.1/2/mbd_nltts_best.csv"



$pir_params$error_measure_params
$pir_params$error_measure_params$burn_in_fraction
[1] 0.1

$pir_params$error_measure_params$error_function
function (tree, trees, distance_method = "abs", ignore_stem = TRUE) 
{
    if (class(tree) != "phylo") {
        stop("'tree' must be of type 'phylo'")
    }
    if (class(trees) != "multiPhylo") {
        stop("'trees' must be of type 'multiPhylo'")
    }
    if (!distance_method %in% c("abs", "squ")) {
        stop("'distance_method' must be either 'abs' or 'squ'")
    }
    if (!ignore_stem %in% c(TRUE, FALSE)) {
        stop("'ignore_stem' must be either TRUE or FALSE")
    }
    nltts <- rep(NULL, length(trees))
    for (i in seq_along(trees)) {
        nltts[i] <- nltt_diff(tree1 = tree, tree2 = trees[[i]], 
            distance_method = distance_method, ignore_stem = ignore_stem)
    }
    nltts
}
<bytecode: 0x561c5a1a5da0>
<environment: namespace:nLTT>


$pir_params$evidence_filename
[1] "/home/p230198/GitHubs/razzo_project/data/0.2-0.15-1-0.1/2/mbd_marg_lik.csv"

$pir_params$verbose
[1] FALSE


$misc_params
$misc_params$tree_filename
[1] "/home/p230198/GitHubs/razzo_project/data/0.2-0.15-1-0.1/2/mbd.tree"

Hypothesis: razzo must call mcbette with a non-Peregrine-friendly working directory

[richelbilderbeek]

Added an extra check before calling pirouette, let's rerun.

[richelbilderbeek]

Maybe the error is upstream, see pirouette Issue 9

[richelbilderbeek]

Fixed with mcbette v1.6